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add branch status job before generating diff and align with cl action (…
…#3283) Co-authored-by: Anita Caron <[email protected]>
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -4,12 +4,14 @@ on: | |
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| issue_comment: | ||
| types: [created] | ||
| env: | ||
| DEFAULT_BRANCH: ${{ github.event.repository.default_branch }} | ||
|
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| # A workflow run is made up of one or more jobs that can run sequentially or in parallel | ||
| jobs: | ||
| diff-reports: | ||
| branch_status: | ||
| if: ${{ github.event.issue.pull_request }} | ||
| runs-on: macos-latest | ||
| runs-on: ubuntu-latest | ||
| permissions: | ||
| contents: read | ||
| pull-requests: read | ||
|
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@@ -20,58 +22,157 @@ jobs: | |
| trigger: '#gogoeditdiff' | ||
| env: | ||
| GITHUB_TOKEN: '${{ secrets.GITHUB_TOKEN }}' | ||
| - uses: better0fdead/actions-setup-docker@better0fdead/increase-timeout | ||
| if: steps.check.outputs.triggered == 'true' | ||
| - run: | | ||
| set -x | ||
| docker version | ||
| if: steps.check.outputs.triggered == 'true' | ||
| - name: Install ODK | ||
| run: docker pull obolibrary/odklite | ||
| if: steps.check.outputs.triggered == 'true' | ||
| # Checks-out current branch | ||
| - uses: xt0rted/pull-request-comment-branch@v2.0.0 | ||
| - uses: xt0rted/pull-request-comment-branch@v2 | ||
| id: comment-branch | ||
| - uses: actions/checkout@v3 | ||
| - uses: actions/checkout@v4 | ||
| if: steps.check.outputs.triggered == 'true' | ||
| with: | ||
| ref: ${{ steps.comment-branch.outputs.head_ref }} | ||
| # Checks-out master branch under "master" directory | ||
| - uses: actions/checkout@v3 | ||
| - uses: actions/checkout@v4 | ||
| if: steps.check.outputs.triggered == 'true' | ||
| with: | ||
| ref: ${{ steps.comment-branch.outputs.head_ref }} | ||
| fetch-depth: 0 | ||
| - name: Check current branch status | ||
| if: steps.check.outputs.triggered == 'true' | ||
| id: info | ||
| run: | | ||
| echo "status=$(git rev-list --left-right --count origin/$DEFAULT_BRANCH...origin/`git branch --show-current` | awk '{print $1}')" | ||
| echo "status=$(git rev-list --left-right --count origin/$DEFAULT_BRANCH...origin/`git branch --show-current` | awk '{print $1}')" >> $GITHUB_OUTPUT | ||
| - name: Warn users with a comment | ||
| if: steps.info.outputs.status >= 1 | ||
| run: echo "Your branch is ${{ steps.info.outputs.status }} commit/s behind, please update your branch." > warncomment.md | ||
| - name: Post comment | ||
| if: steps.info.outputs.status >= 1 && steps.check.outputs.triggered == 'true' | ||
| env: | ||
| GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}} | ||
| uses: NejcZdovc/comment-pr@v2 | ||
| with: | ||
| github_token: ${{secrets.GITHUB_TOKEN}} | ||
| file: "../../warncomment.md" | ||
| - name: Fail step if branch is behind | ||
| if: steps.info.outputs.status >= 1 && steps.check.outputs.triggered == 'true' | ||
| run: | | ||
| echo "Your branch is ${{ steps.info.outputs.status }} commit/s behind, please update your branch." | ||
| exit 1 | ||
| edit_file: | ||
| needs: [branch_status] | ||
| if: ${{ github.event.issue.pull_request }} | ||
| runs-on: ubuntu-latest | ||
| container: obolibrary/odkfull:v1.5 | ||
| steps: | ||
| - uses: khan/[email protected] | ||
| id: check | ||
| with: | ||
| trigger: '#gogoeditdiff' | ||
| env: | ||
| GITHUB_TOKEN: '${{ secrets.GITHUB_TOKEN }}' | ||
| - uses: actions/checkout@v4 | ||
| if: steps.check.outputs.triggered == 'true' | ||
| with: | ||
| ref: master | ||
| path: master | ||
| - name: Diff classification | ||
| if: steps.check.outputs.triggered == 'true' | ||
| run: | | ||
| cd src/ontology | ||
| docker run -v $PWD/../../:/work -w /work/src/ontology -e ROBOT_JAVA_ARGS='-Xmx9G' -e JAVA_OPTS='-Xmx9G' --rm obolibrary/odklite robot diff --left ../../master/src/ontology/uberon-edit.obo --left-catalog ../../master/src/ontology/catalog-v001.xml --right uberon-edit.obo --right-catalog catalog-v001.xml -f markdown -o edit-diff.md | ||
| run: export ROBOT_JAVA_ARGS='-Xmx9G'; robot diff --labels True --left master/src/ontology/uberon-edit.obo --left-catalog master/src/ontology/catalog-v001.xml --right branch/src/ontology/uberon-edit.obo --right-catalog branch/src/ontology/catalog-v001.xml -f markdown -o edit-diff.md | ||
| - name: Upload diff | ||
| if: steps.check.outputs.triggered == 'true' | ||
| uses: actions/upload-artifact@v3 | ||
| uses: actions/upload-artifact@v4 | ||
| with: | ||
| name: edit-diff.md | ||
| path: src/ontology/edit-diff.md | ||
| - name: Make step for branch | ||
| path: edit-diff.md | ||
| classify_branch: | ||
| needs: [branch_status] | ||
| if: ${{ github.event.issue.pull_request }} | ||
| runs-on: ubuntu-latest | ||
| container: obolibrary/odkfull:v1.5 | ||
| steps: | ||
| - uses: khan/[email protected] | ||
| id: check | ||
| with: | ||
| trigger: '#gogoeditdiff' | ||
| env: | ||
| GITHUB_TOKEN: '${{ secrets.GITHUB_TOKEN }}' | ||
| - uses: xt0rted/pull-request-comment-branch@v2 | ||
| id: comment-branch | ||
| - uses: actions/checkout@v4 | ||
| if: steps.check.outputs.triggered == 'true' | ||
| run: cd src/ontology && mkdir -p tmp reports mirror && docker run -v $PWD/../../:/work -w /work/src/ontology -e ROBOT_JAVA_ARGS='-Xmx9G' -e JAVA_OPTS='-Xmx9G' --rm obolibrary/odklite make BRI=false MIR=false PAT=false IMP=false uberon-simple.owl > TESTLOG.log | ||
| - name: Make step for master | ||
| with: | ||
| ref: ${{ steps.comment-branch.outputs.head_ref }} | ||
| - name: Classify ontology PR branch | ||
| if: steps.check.outputs.triggered == 'true' | ||
| run: cd master/src/ontology && mkdir -p tmp reports mirror && docker run -v $PWD/../../:/work -w /work/src/ontology -e ROBOT_JAVA_ARGS='-Xmx9G' -e JAVA_OPTS='-Xmx9G' --rm obolibrary/odklite make BRI=false MIR=false PAT=false IMP=false uberon-simple.owl > TESTLOG.log | ||
| - name: Diff report | ||
| run: export ROBOT_JAVA_ARGS='-Xmx9G'; cd src/ontology; make BRI=false MIR=false PAT=false IMP=false COMP=false uberon-base.owl > TESTLOG.log | ||
| - name: Upload classified ontology in PR branch | ||
| if: steps.check.outputs.triggered == 'true' | ||
| run: | | ||
| cd src/ontology | ||
| docker run -v $PWD/../../:/work -w /work/src/ontology -e ROBOT_JAVA_ARGS='-Xmx9G' -e JAVA_OPTS='-Xmx9G' --rm obolibrary/odklite robot diff --left ../../master/src/ontology/uberon-simple.owl --left-catalog catalog-v001.xml --right uberon-simple.owl --right-catalog ../../master/src/ontology/catalog-v001.xml -f markdown -o simple-report.md | ||
| uses: actions/upload-artifact@v4 | ||
| with: | ||
| name: uberon-base-pr.owl | ||
| path: src/ontology/uberon-base.owl | ||
| retention-days: 1 | ||
| classify_main: | ||
| needs: [branch_status] | ||
| if: ${{ github.event.issue.pull_request }} | ||
| runs-on: ubuntu-latest | ||
| container: obolibrary/odkfull:v1.5 | ||
| steps: | ||
| - uses: khan/[email protected] | ||
| id: check | ||
| with: | ||
| trigger: '#gogoeditdiff' | ||
| env: | ||
| GITHUB_TOKEN: '${{ secrets.GITHUB_TOKEN }}' | ||
| - uses: actions/checkout@v4 | ||
| if: steps.check.outputs.triggered == 'true' | ||
| with: | ||
| ref: master | ||
| - name: Classify ontology main branch | ||
| if: steps.check.outputs.triggered == 'true' | ||
| run: export ROBOT_JAVA_ARGS='-Xmx9G'; cd src/ontology; make BRI=false MIR=false PAT=false IMP=false COMP=false uberon-base.owl > TESTLOG.log | ||
| - name: Upload classified ontology main branch | ||
| if: steps.check.outputs.triggered == 'true' | ||
| uses: actions/upload-artifact@v4 | ||
| with: | ||
| name: uberon-base-main.owl | ||
| path: src/ontology/uberon-base.owl | ||
| retention-days: 1 | ||
| diff_classification: | ||
| needs: [classify_branch, classify_main] | ||
| runs-on: ubuntu-latest | ||
| container: obolibrary/odkfull:v1.5 | ||
| steps: | ||
| - uses: khan/[email protected] | ||
| id: check | ||
| with: | ||
| trigger: '#gogoeditdiff' | ||
| env: | ||
| GITHUB_TOKEN: '${{ secrets.GITHUB_TOKEN }}' | ||
| - uses: actions/checkout@v4 | ||
| if: steps.check.outputs.triggered == 'true' | ||
| - name: Download classified ontology main branch | ||
| if: steps.check.outputs.triggered == 'true' | ||
| uses: actions/download-artifact@v4 | ||
| with: | ||
| name: uberon-base-main.owl | ||
| path: src/ontology/uberon-base-main.owl | ||
| - name: Download classified ontology in PR branch | ||
| if: steps.check.outputs.triggered == 'true' | ||
| uses: actions/download-artifact@v4 | ||
| with: | ||
| name: uberon-base-pr.owl | ||
| path: src/ontology/uberon-base-pr.owl | ||
| - name: Diff classification | ||
| if: steps.check.outputs.triggered == 'true' | ||
| run: export ROBOT_JAVA_ARGS='-Xmx9G'; cd src/ontology; robot diff --labels True --left uberon-base-main.owl/uberon-base.owl --left-catalog catalog-v001.xml --right uberon-base-pr.owl/uberon-base.owl --right-catalog catalog-v001.xml -f markdown -o classification-diff.md | ||
| - name: Upload diff | ||
| if: steps.check.outputs.triggered == 'true' | ||
| uses: actions/upload-artifact@v3 | ||
| uses: actions/upload-artifact@v4 | ||
| with: | ||
| name: simple-report.md | ||
| path: src/ontology/simple-report.md | ||
| name: classification-diff.md | ||
| path: src/ontology/classification-diff.md | ||
| post_comment: | ||
| needs: [diff-reports] | ||
| needs: [edit_file, diff_classification] | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - uses: khan/[email protected] | ||
|
|
@@ -80,33 +181,34 @@ jobs: | |
| trigger: '#gogoeditdiff' | ||
| env: | ||
| GITHUB_TOKEN: '${{ secrets.GITHUB_TOKEN }}' | ||
| - uses: actions/checkout@v3 | ||
| - uses: actions/checkout@v4 | ||
| if: steps.check.outputs.triggered == 'true' | ||
| - name: Download reasoned diff | ||
| if: steps.check.outputs.triggered == 'true' | ||
| uses: actions/download-artifact@v3 | ||
| uses: actions/download-artifact@v4 | ||
| with: | ||
| name: simple-report.md | ||
| name: classification-diff.md | ||
| - name: Prepare reasoned comment | ||
| run: "echo \"<details>\n <summary> Here's a diff of how these changes impact the classified ontology (on -simple file): </summary> \n\" > comment.md; cat simple-report.md >> comment.md" | ||
| if: steps.check.outputs.triggered == 'true' | ||
| run: "echo \"<details>\n <summary> Here's a diff of how these changes impact the classified ontology (on -base file): </summary> \n\" > comment.md; cat classification-diff.md >> comment.md" | ||
| - name: Post reasoned comment | ||
| if: steps.check.outputs.triggered == 'true' | ||
| uses: NejcZdovc/[email protected] | ||
| with: | ||
| file: "../../comment.md" | ||
| identifier: "REASONED" | ||
| github_token: ${{secrets.GITHUB_TOKEN}} | ||
| - uses: actions/checkout@v3 | ||
| - uses: actions/checkout@v4 | ||
| if: steps.check.outputs.triggered == 'true' | ||
| - name: Download edit diff | ||
| if: steps.check.outputs.triggered == 'true' | ||
| uses: actions/download-artifact@v2 | ||
| uses: actions/download-artifact@v4 | ||
| with: | ||
| name: edit-diff.md | ||
| path: edit-diff.md | ||
| - name: Prepare edit file comment | ||
| run: "echo \"<details>\n <summary> Here's a diff of your edit file (unreasoned) </summary> \n\" > edit-comment.md; cat edit-diff.md >> edit-comment.md" | ||
| if: steps.check.outputs.triggered == 'true' | ||
| run: "echo \"<details>\n <summary> Here's a diff of your edit file (unreasoned) </summary> \n\" > edit-comment.md; cat edit-diff.md >> edit-comment.md" | ||
| - name: Post comment | ||
| if: steps.check.outputs.triggered == 'true' | ||
| uses: NejcZdovc/[email protected] | ||
|
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